I want to quantify gene expression for my Trinity transcriptome assembly using RSEM. I am getting confusing results depending on how I specify quality scores of the Illumina paired end reads. They are Illumina 1.5 and have phred 64 quality scores.

RSEM does not ignore quality scores. It uses the quality scores to help
it allocate multi-mapping reads. But when RSEM calls Bowtie2, we set the
Bowtie2 parameters in a way that ignores quality scores. In particular,
we set '--mp 1,1', which implies a mismatch penalty of 1 regardless of
the quality score.